XNAT Pipeline-engine is a Java-based workflow framework nicely integrated (that's basically its inception purpose) in XNAT. Pipeline-engine uses XML-based workflow definitions for processing data hosted in XNAT by linking sequential activities or steps.
- Provides mechanisms for batch-mode triggering pipeline instances (via REST API).
- Enables submission of jobs to a Distributed Resource Management (DRM) system supporting the Distributed Resource Management Application API (DRMAA) specification, e.g. SGE.
XNAT pipelines repository, see the wishlist for incomming apps.
- ExamCard extractor :: Extracts Philips ExamCard objects embedded in DICOM object files
- FreeSurfer :: FreeSurfer recon-all pipeline with XNAT assessor output with stats metrics
- mricron :: DICOM and PARREC flavoured pipelines for imaging data conversion to NIFTI format (using dcm2nii)
- Quality Assessment Protocol :: QA analysis on functional/structural MRI data
- mricrogl :: New generation of DICOM-to-NIFTI format conversion pipeline (using dcm2niix)
- DTI-preprocessing :: Compute preprocessing corrections on MRI DTI scans
- MRI bias field correction :: correcting intensity non-uniformity (i.e. bias fields)
- MRI anatomical defacer :: Automated facial traits removal (defacing) of anatomical scan data.
- qMRI :: Calculate quantitative anatomical MRI (qMRI) mapping. qMRI provides MRI measures that are comparable across sites and time points. More background here.
Jordi Huguet, Department of Neuroradiology & Brain Imaging Centre, AMC-UvA Amsterdam
This work is licensed under the terms of the GNU GPLv3 license.